GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Xenophilus azovorans DSM 13620

Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_051953036.1 Q392_RS06860 glutamine amidotransferase

Query= curated2:P05379
         (204 letters)



>NCBI__GCF_000745855.1:WP_051953036.1
          Length = 254

 Score = 42.7 bits (99), Expect = 6e-09
 Identities = 32/106 (30%), Positives = 45/106 (42%), Gaps = 16/106 (15%)

Query: 86  PILGVCLGHQAIGAAFGGKVVPAPV-----LMHGKVSPIHHDGTGVFRGLDSPFPATRYH 140
           P+LG+C GHQ +  A GG+    P+      +  ++ P   +G  +  GL   F A   H
Sbjct: 98  PVLGICYGHQLLADALGGRADDHPLGREVGTVEVELLP-EAEGDALMAGLPPRFAAQVVH 156

Query: 141 SLAVVEVPE---ALVVNAWAEEAGGRTVMGFRHRDYPTHGVQFHPE 183
             + + +P    AL  NAW      R             GVQFHPE
Sbjct: 157 RQSALALPPGAVALARNAWEPHQAVRF-------GEAAWGVQFHPE 195


Lambda     K      H
   0.322    0.141    0.445 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 138
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 204
Length of database: 254
Length adjustment: 22
Effective length of query: 182
Effective length of database: 232
Effective search space:    42224
Effective search space used:    42224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory